cellpose

cellpose is an anatomical segmentation algorithm written in Python 3 by Carsen Stringer and Marius Pachitariu. For support, please open an issue.

We make pip installable releases of cellpose, here is the pypi. You can install it as pip install cellpose[gui].

You can try it out without installing at cellpose.org. Also check out these resources:

twitter thread
Marius's talk on cellpose
paper on biorxiv (see figure 1 below)

.. toctree::
   :maxdepth: 3
   :caption: Basics:

   installation
   gui
   inputs
   settings
   outputs
   train

.. toctree::
   :maxdepth: 3
   :caption: Examples:

   notebook
   command

.. toctree::
   :caption: API Reference:

   api